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Structure of DexA reveal the novel Mechanism of DNA catalysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other AF-A0A2M9X318-F1-model-v4 We used the structure that predicted by AlphaFold as the searching model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.02M Calcium chloride dihydrate, 0.1M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 3.34 63.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.548 α = 90 b = 76.285 β = 93.36 c = 108.009 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 9M 2022-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9791 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.88 35.94 95.96 0.99 8.25 4 30240 70.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 2.98 0.704
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.88 35.94 1.35 30056 1434 96.03 0.225 0.2225 0.2762 0.3017 83.85
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.2162 f_angle_d 1.082 f_chiral_restr 0.0584 f_plane_restr 0.0098 f_bond_d 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6550 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing